Objective
| Sample.1 | Sample.2 | Sample.3 | Sample.4 | |
|---|---|---|---|---|
| chr1:1:100 | 19 | 24 | 12 | 14 |
| chr2:101:200 | 25 | 23 | 17 | 18 |
| chr1:201:300 | 20 | 27 | 12 | 18 |
| chr2:301:400 | 19 | 25 | 16 | 10 |
| chr2:401:500 | 17 | 27 | 14 | 25 |
\(x_{i,j}=\frac{WindowCoverage_{i,j}\times10^{9}}{WindowLength_{i}\times{totalReadsSample_{j}}}\)
\(xnorm_{i,j}=\frac{x_{i,j}}{mean(X_{i})}\)
\(x_{i,j}=\frac{WindowCoverage_{i,j}\times10^{9}}{WindowLength_{i}\times{totalReadsSample_{j}}}\)
| Sample.1 | Sample.2 | Sample.3 | Sample.4 | |
|---|---|---|---|---|
| chr1:1:100 | 19 | 24 | 12 | 14 |
| chr2:101:200 | 25 | 23 | 17 | 18 |
| chr1:201:300 | 20 | 27 | 12 | 18 |
| chr2:301:400 | 19 | 25 | 16 | 10 |
| chr2:401:500 | 17 | 27 | 14 | 25 |
| totalReadsSample | 100 | 126 | 71 | 85 |
\(xnorm_{i,j}=\frac{x_{i,j}}{mean(X_{i})}\)
| Sample.1 | Sample.2 | Sample.3 | Sample.4 | Window Mean | |
|---|---|---|---|---|---|
| chr1:1:100 | 1919192 | 1924002 | 1707213 | 1663696 | 1803526 |
| chr2:101:200 | 2525253 | 1843835 | 2418552 | 2139037 | 2231669 |
| chr1:201:300 | 2020202 | 2164502 | 1707213 | 2139037 | 2007739 |
| chr2:301:400 | 1919192 | 2004169 | 2276284 | 1188354 | 1847000 |
| chr2:401:500 | 1717172 | 2164502 | 1991748 | 2970885 | 2211077 |
| Sample.1 | Sample.2 | Sample.3 | Sample.4 | |
|---|---|---|---|---|
| chr1:1:100 | 1.0641334 | 1.0668004 | 0.9465976 | 0.9224686 |
| chr2:101:200 | 1.1315532 | 0.8262135 | 1.0837411 | 0.9584922 |
| chr1:201:300 | 1.0062077 | 1.0780796 | 0.8503163 | 1.0653964 |
| chr2:301:400 | 1.0390862 | 1.0850942 | 1.2324225 | 0.6433970 |
| chr2:401:500 | 0.7766223 | 0.9789357 | 0.9008047 | 1.3436373 |
5 out of 823 lines are noisy (\(\sigma > 0.45\)).
| line | SD |
|---|---|
| WATDE0009 | 0.75 |
| WATDE0039 | 1.08 |
| WATDE0056 | 0.51 |
| WATDE0060 | 0.52 |
| WATDE0090 | 0.50 |
Can we get an overview across a line?
There are 43,412,060 CNV events across 823 lines
22,294,613 (51.36 %) are not singletons